Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOXA1

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MCF7L breast cancer cell line
antibody
FOXA1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
chromatin from approximately 1 × 107 fixed cells was sonicated to a size range of 200-300 bp. Solubilized chromatin was subjected to immunoprecipitation with the FOXA1 antibody bound to protein A and protein G beads. A fraction of the sample was not exposed to antibody to be used as control (input). The samples were reversed crosslinked, treated with proteinase K, and DNA was extracted. DNA sequencing libraries were prepared using the ThruPLEX-FD Prep Kit (Rubicon Genomics). Libraries were sequenced using 50-bp reads on the Illumina platform DNA sequencing libraries were prepared using the ThruPLEX-FD Prep Kit (Rubicon Genomics per manual). Libraries were sequenced using Illumina platform

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
37931530
Reads aligned (%)
69.9
Duplicates removed (%)
20.5
Number of peaks
33717 (qval < 1E-05)

hg38

Number of total reads
37931530
Reads aligned (%)
72.0
Duplicates removed (%)
19.0
Number of peaks
34176 (qval < 1E-05)

Base call quality data from DBCLS SRA